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Multiannual patterns of influenza A transmission in Chinese live bird market systems.

Pepin KM, Wang J, Webb CT, Smith GJ, Poss M, Hudson PJ, Hong W, Zhu H, Riley S, Guan Y - Influenza Other Respir Viruses (2012)

Bottom Line: However, predicting AIV epizootics and emergence in humans is confounded by insufficient empirical data on the ecology and dynamics of AIV in poultry systems.No significant seasonality was found when all subtypes were considered together.Quantitative models of control strategies must consider multiple subtypes, hosts, and source contexts to assess the effectiveness of interventions.

View Article: PubMed Central - PubMed

Affiliation: International Institution of Infection and Immunity, Shantou University Medical College, Shantou, China Colorado State University, Fort Collins, CO, USA.

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 Patterns of host usage and context dependence. A shows host usage for host species that were sampled consistently over the longest time period. Only the last 3 years of retail market data (September 2003–September 2006) were included because this was the time period during which the most host species were sampled consistently (see Figure S1) and surveillance protocols were unchanged. Context dependence patterns for subtypes are shown in ducks (B) and chickens (C). Farms were excluded in C because chickens were not sampled intensely enough (see Figure S2). Gray boxes indicate a significantly positive relationship, black boxes are for significantly negative relationships, and white boxes indicate that the infection rate is proportional to the number of samples collected. Numbers inside the boxes: # of positive samples, number of monthly time points in analysis. Only subtypes for which there were adequate samples, and host species that were sampled consistently, were included in the analysis. Hosts are listed across the top (abbreviations as in Table 1). Subtypes are listed in the first column; Avian Paramyxovirus‐type‐1 is Avian Paramyxovirus‐type‐1. The total number of samples collected from each host species is listed along the bottom. The total number of positive samples for each subtype is in the last column. For each subtype, we excluded time points in which no positive samples were found (reflected in the second number in each box). Bird groups with multiple subspecies from the same species were pooled in A (a preliminary analysis showed that there were no differences between these groups). Alpha values were adjusted for multiple tests using a Bonferroni correction (αA = 0.0071, αB = 0.0167, αC = 0.025).
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f3:  Patterns of host usage and context dependence. A shows host usage for host species that were sampled consistently over the longest time period. Only the last 3 years of retail market data (September 2003–September 2006) were included because this was the time period during which the most host species were sampled consistently (see Figure S1) and surveillance protocols were unchanged. Context dependence patterns for subtypes are shown in ducks (B) and chickens (C). Farms were excluded in C because chickens were not sampled intensely enough (see Figure S2). Gray boxes indicate a significantly positive relationship, black boxes are for significantly negative relationships, and white boxes indicate that the infection rate is proportional to the number of samples collected. Numbers inside the boxes: # of positive samples, number of monthly time points in analysis. Only subtypes for which there were adequate samples, and host species that were sampled consistently, were included in the analysis. Hosts are listed across the top (abbreviations as in Table 1). Subtypes are listed in the first column; Avian Paramyxovirus‐type‐1 is Avian Paramyxovirus‐type‐1. The total number of samples collected from each host species is listed along the bottom. The total number of positive samples for each subtype is in the last column. For each subtype, we excluded time points in which no positive samples were found (reflected in the second number in each box). Bird groups with multiple subspecies from the same species were pooled in A (a preliminary analysis showed that there were no differences between these groups). Alpha values were adjusted for multiple tests using a Bonferroni correction (αA = 0.0071, αB = 0.0167, αC = 0.025).

Mentions: H1, H3, H4, and H11 were overrepresented in ducks and underrepresented in all other host species, whereas H5, H6, H9, and APMV‐1 showed different, more inclusive host usage patterns (Figure 3A). H5 showed the most non‐specific host usage pattern with its random association to all hosts except for an underrepresentation in chukars and pigeons (i.e., where random association means that the subtype infects host species X in proportion with the number of samples from host species X). H6 was randomly associated with ducks and quail, overrepresented in chukars, and underrepresented in chickens, pheasants, and pigeons. H9 was overrepresented in quail and chickens, underrepresented in ducks, chukars, and pigeons, and randomly associated with pheasants and guinea fowl. APMV‐1 was overrepresented in chickens and underrepresented all other hosts except pigeons and guinea fowl where it was randomly associated. Although we were unable to include partridge in the host usage analysis (because of a difference in sampling time relative to other hosts), the infection results are worth noting because infection rates in partridge were the highest for any host species at 27·3% (Table 1). Almost all of the infections in partridge included H5 (6·4%), H6 (17·7%), H9 (73·5%), and APMV‐1 (8·4%) (Table S1). Similarly, these four subtypes caused most of the infections in other minor poultry species: pheasant, chukar, partridge, and guinea fowl (Table S1). H5 was most prevalent and caused the highest number of infections of any subtype, in domestic geese.


Multiannual patterns of influenza A transmission in Chinese live bird market systems.

Pepin KM, Wang J, Webb CT, Smith GJ, Poss M, Hudson PJ, Hong W, Zhu H, Riley S, Guan Y - Influenza Other Respir Viruses (2012)

 Patterns of host usage and context dependence. A shows host usage for host species that were sampled consistently over the longest time period. Only the last 3 years of retail market data (September 2003–September 2006) were included because this was the time period during which the most host species were sampled consistently (see Figure S1) and surveillance protocols were unchanged. Context dependence patterns for subtypes are shown in ducks (B) and chickens (C). Farms were excluded in C because chickens were not sampled intensely enough (see Figure S2). Gray boxes indicate a significantly positive relationship, black boxes are for significantly negative relationships, and white boxes indicate that the infection rate is proportional to the number of samples collected. Numbers inside the boxes: # of positive samples, number of monthly time points in analysis. Only subtypes for which there were adequate samples, and host species that were sampled consistently, were included in the analysis. Hosts are listed across the top (abbreviations as in Table 1). Subtypes are listed in the first column; Avian Paramyxovirus‐type‐1 is Avian Paramyxovirus‐type‐1. The total number of samples collected from each host species is listed along the bottom. The total number of positive samples for each subtype is in the last column. For each subtype, we excluded time points in which no positive samples were found (reflected in the second number in each box). Bird groups with multiple subspecies from the same species were pooled in A (a preliminary analysis showed that there were no differences between these groups). Alpha values were adjusted for multiple tests using a Bonferroni correction (αA = 0.0071, αB = 0.0167, αC = 0.025).
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f3:  Patterns of host usage and context dependence. A shows host usage for host species that were sampled consistently over the longest time period. Only the last 3 years of retail market data (September 2003–September 2006) were included because this was the time period during which the most host species were sampled consistently (see Figure S1) and surveillance protocols were unchanged. Context dependence patterns for subtypes are shown in ducks (B) and chickens (C). Farms were excluded in C because chickens were not sampled intensely enough (see Figure S2). Gray boxes indicate a significantly positive relationship, black boxes are for significantly negative relationships, and white boxes indicate that the infection rate is proportional to the number of samples collected. Numbers inside the boxes: # of positive samples, number of monthly time points in analysis. Only subtypes for which there were adequate samples, and host species that were sampled consistently, were included in the analysis. Hosts are listed across the top (abbreviations as in Table 1). Subtypes are listed in the first column; Avian Paramyxovirus‐type‐1 is Avian Paramyxovirus‐type‐1. The total number of samples collected from each host species is listed along the bottom. The total number of positive samples for each subtype is in the last column. For each subtype, we excluded time points in which no positive samples were found (reflected in the second number in each box). Bird groups with multiple subspecies from the same species were pooled in A (a preliminary analysis showed that there were no differences between these groups). Alpha values were adjusted for multiple tests using a Bonferroni correction (αA = 0.0071, αB = 0.0167, αC = 0.025).
Mentions: H1, H3, H4, and H11 were overrepresented in ducks and underrepresented in all other host species, whereas H5, H6, H9, and APMV‐1 showed different, more inclusive host usage patterns (Figure 3A). H5 showed the most non‐specific host usage pattern with its random association to all hosts except for an underrepresentation in chukars and pigeons (i.e., where random association means that the subtype infects host species X in proportion with the number of samples from host species X). H6 was randomly associated with ducks and quail, overrepresented in chukars, and underrepresented in chickens, pheasants, and pigeons. H9 was overrepresented in quail and chickens, underrepresented in ducks, chukars, and pigeons, and randomly associated with pheasants and guinea fowl. APMV‐1 was overrepresented in chickens and underrepresented all other hosts except pigeons and guinea fowl where it was randomly associated. Although we were unable to include partridge in the host usage analysis (because of a difference in sampling time relative to other hosts), the infection results are worth noting because infection rates in partridge were the highest for any host species at 27·3% (Table 1). Almost all of the infections in partridge included H5 (6·4%), H6 (17·7%), H9 (73·5%), and APMV‐1 (8·4%) (Table S1). Similarly, these four subtypes caused most of the infections in other minor poultry species: pheasant, chukar, partridge, and guinea fowl (Table S1). H5 was most prevalent and caused the highest number of infections of any subtype, in domestic geese.

Bottom Line: However, predicting AIV epizootics and emergence in humans is confounded by insufficient empirical data on the ecology and dynamics of AIV in poultry systems.No significant seasonality was found when all subtypes were considered together.Quantitative models of control strategies must consider multiple subtypes, hosts, and source contexts to assess the effectiveness of interventions.

View Article: PubMed Central - PubMed

Affiliation: International Institution of Infection and Immunity, Shantou University Medical College, Shantou, China Colorado State University, Fort Collins, CO, USA.

Show MeSH
Related in: MedlinePlus